Hi,

I am using ont_guppy_duplex_pipeline to re-base-call raw data from ONT sequencing. I am invoking full pipeline by simplex base-calling in fast mode, then duplex calling with sup mode and finally base-calling of all reads that were not in simplex base-calling with sup mode again. The problem is that it seems the duplex base-calling does not fetch the correct parameters and aborts with an error. Normally, the duplex base-calling requires two parameters:

--duplex_pairing_mode from_pair_list --duplex_pairing_file <text pair file>

to function but to my understanding there is no where in the command arguments to set that. Here is the output of help:

guppy_duplex -h usage: guppy_duplex [-h] [--basecaller_exe BASECALLER_EXE] [--duplex_basecaller_exe DUPLEX_BASECALLER_EXE] --input_path INPUT_PATH
                --save_path SAVE_PATH [--simplex_config SIMPLEX_CONFIG] [--duplex_config DUPLEX_CONFIG] [--disable_logging]
                [--skip_simplex] [--skip_duplex] [--call_non_duplex_reads] [--device DEVICE] [--do_read_splitting]
                [--duplex_chunks_per_runner DUPLEX_CHUNKS_PER_RUNNER] [--recursive]

And here is my code for running the pipe that breaks when duplex calling starts. I must add that simplex calling completes successfully.

 guppy_duplex -i ./pod5/ -s ./output2/ --simplex_config dna_r10.4.1_e8.2_400bps_fast.cfg --duplex_config  dna_r10.4.1_e8.2_400bps_sup.cfg --device 'cuda:0'

This is how the pipeline fails:

I appreciate if someone with the knowledge, helps with this.